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At least 19 records

BOREAS Forest Cover Data Layers of the NSA in Raster Format

This data set was processed by BORIS staff from the original vector data of species, crown closure, cutting class, and site classification/subtype into raster files. The original polygon data were received from Linnet Graphics, the distributor of data for MNR. In the case of the species layer, the percentages of species composition were removed. This reduced the amount of information contained in the species layer of the gridded product, but it was necessary in order to make the gridded product easier to use. The original maps were produced from 1:15,840-scale aerial photography collected in 1988 over an area of the BOREAS NSA MSA. The data are stored in binary, image format files and they are available from Oak Ridge National Laboratory. The data files are available on a CD-ROM (see document number 20010000884).

Hall, Forrest G.↗

Mesophyll conductance response to short-term changes in p CO 2 is related to leaf anatomy and biochemistry in diverse C 4 grasses

Mesophyll CO 2 conductance (g m ) in C 3 species responds to short-term (minutes) changes in environment potentially due to changes in leaf anatomical and biochemical properties and measurement artefacts. Compared with C 3 species, there is less information on g m responses to short-term changes in environmental conditions such as partial pressure of CO 2 (pCO 2 ) across diverse C 4 species and the potential determinants of these responses. Using 16 C 4 grasses we investigated the response of g m to short-term changes in pCO 2 and its relationship with leaf anatomy and biochemistry. In general, g m increased as pCO 2 decreased (statistically significant increase in 12 species), with percentage increases in gm ranging from +13% to +250%. Greater increase in g m at low pCO 2 was observed in species exhibiting relatively thinner mesophyll cell walls along with greater mesophyll surface area exposed to intercellular air spaces, leaf N, photosynthetic capacity and activities of phosphoenolpyruvate carboxylase and Rubisco. Species with greater CO 2 responses of g m were also able to maintain their leaf water-use efficiencies (TE i ) under low CO 2 . Our study advances understanding of CO 2 response of g m in diverse C 4 species, identifies the key leaf traits related to this response and has implications for improving C 4 photosynthetic models and TE i through modification of g m .

59 BASIC BIOLOGICAL SCIENCES↗

Enumerating soil biodiversity

Soil is an immense habitat for diverse organisms across the tree of life, but just how many organisms live in soil is surprisingly unknown. Previous efforts to enumerate soil biodiversity consider only certain types of organisms (e.g., animals) or report values for diverse groups without partitioning species that live in soil versus other habitats. Here, we reviewed the biodiversity literature to show that soil is likely home to 59 ± 15% of the species on Earth. We therefore estimate an approximately two times greater soil biodiversity than previous estimates, and we include representatives from the simplest (microbial) to most complex (mammals) organisms. Enchytraeidae have the greatest percentage of species in soil (98.6%), followed by fungi (90%), Plantae (85.5%), and Isoptera (84.2%). Our results demonstrate that soil is the most biodiverse singular habitat. By using this estimate of soil biodiversity, we can more accurately and quantitatively advocate for soil organismal conservation and restoration as a central goal of the Anthropocene.

Science & Technology - Other Topics↗

Mapping coastal vegetation, land use and environmental impact from ERTS-1

The author has identified the following significant results. Vegetation map overlays at a scale of 1:24,000 compiled by multispectral analysis from NASA aircraft imagery for all of Delaware's wetlands are being used as ground truth for ERTS-1 mapping and by state agencies for wetlands management. Six major vegetation species were discriminated and mapped, including percentages of minor species. Analogue enhancements of wetlands vegetation and dredge-fill operations have been produced using General Electric's GEMS data processing and ERTS-1 false color composites. Digital, thematic land use, and vegetation mapping of entire Delaware Bay area is in progress using Bendix Corporation's Earth Resources Data System and ERTS-1 digital tapes. Statistical evaluation of target-group selection reliability has been completed. Three papers have been published on ERTS-1 coastal vegetation and land use. Local and state officials are participating in the ERTS-1 program as co-investigators.

Klemas, V.↗

Simulating Forest Dynamics of Lowland Rainforests in Eastern Madagascar

Ecological modeling and forecasting are essential tools for the understanding of complex vegetation dynamics. The parametric demands of some of these models are often lacking or scant for threatened ecosystems, particularly in diverse tropical ecosystems. One such ecosystem and also one of the world's biodiversity hotspots, Madagascar's lowland rainforests, have disappeared at an alarming rate. The processes that drive tree species growth and distribution remain as poorly understood as the species themselves. We investigated the application of the process-based individual-based FORMIND model to successfully simulate a Madagascar lowland rainforest using previously collected multi-year forest inventory plot data. We inspected the model's ability to characterize growth and species abundance distributions over the study site, and then validated the model with an independently collected forest-inventory dataset from another lowland rainforest in eastern Madagascar. Following a comparative analysis using inventory data from the two study sites, we found that FORMIND accurately captures the structure and biomass of the study forest, with r(squared) values of 0.976, 0.895, and 0.995 for 1:1 lines comparing observed and simulated values across all plant functional types for aboveground biomass (tonnes/ha), stem numbers, and basal area (m(squared)/ha), respectively. Further, in validation with a second study forest site, FORMIND also compared well, only slightly over-estimating shade-intermediate species as compared to the study site, and slightly under-representing shade-tolerant species in percentage of total aboveground biomass. As an important application of the FORMIND model, we measured the net ecosystem exchange (NEE, in tons of carbon per hectare per year) for 50 ha of simulated forest over a 1000-year run from bare ground. We found that NEE values ranged between 1 and -1 t Cha(exp -1)year(exp -1), consequently the study forest can be considered as a net neutral or a very slight carbon sink ecosystem, after the initial 130 years of growth. Our study found that FORMIND represents a valuable tool toward simulating forest dynamics in the immensely diverse Madagascar rainforests.

Forest Productivity↗

Probing Active-Site Relocation in Cu/SSZ-13 SCR Catalysts during Hydrothermal Aging by in situ EPR Spectroscopy, Kinetic Studies, and DFT Calculations

Cu/SSZ-13 selective catalytic reduction catalysts display activity loss after mild hydrothermal aging without support degradation or loss of isolated Cu ion content. By applying electron paramagnetic resonance spectroscopy to compare hydrated, dehydrated and NH3-saturated catalysts before and after hydrothermal aging, as well as density functional theory calculations, it is found that hydrothermal aging induces Cu relocation, leading to stronger Cu-support interactions. This is particularly evidenced by ZCuOH conversion to Z2Cu, which leads to the generation of a unique structure with two Cu(II) ions positioned in a double 6-membered ring prism. The Cu(II) ions that do not undergo such dramatic changes also appear to stay closer to framework windows as evidenced by the overall increased anisotropy during EPR measurements. In situ EPR measurements under SCR conditions demonstrate that, in comparison to the fresh catalyst, higher percentages of Cu species stay as Cu(II) in the aged catalyst. This suggests that the reduction half-cycle of the SCR redox, i.e., Cu(II) ? Cu(I), becomes slower for the hydrothermally aged catalyst.

42 ENGINEERING↗

Investigation of Prophage Regions of Bacterial Strains Isolated from the International Space Station (ISS)

Space flight agencies are planning missions back to the Moon and to Mars. When sending humans into space, it is impossible to separate them from microorganisms, either in their associated microbiome or in the spacecraft environment, which are modified through the movement of genetic material. Bacteriophages, small viruses that invade and replicate within bacterial cells, play a central role in the genetic composition and evolution of microorganisms. Lysogenic bacteriophages can insert themselves into the DNA of their bacterial hosts, forming prophage regions, which can also transfer genes from previous hosts. Thus, we aimed to identify and classify all prophages from twelve bacterial species cultured from the International Space Station (ISS) from 2017 to 2018. We determined representative bacterial strains for each species, whose genomes were analyzed to identify prophage regions. Complete prophages were identified through database searches and the number of prophage regions were compared to terrestrial analogs. Additionally, prophage region and genome sizes were compared for each species, identifying the percentage of bacteriophage DNA in each genome. We determined that the prophage-susceptible bacterial species isolated from the ISS had a higher number of prophage regions when compared to terrestrial analogs, as well as having a larger percentage of their genomes made up of prophage material. Of the eighteen complete prophages identified, 72.2% were of family Siphoviridae and 27.8% were of family Myoviridae. Only one of the prophages had a BLAST similarity over 80%, suggesting that the remainder of prophages are novel species. These results imply that there is a higher rate of prophage transduction and lysogeny during spaceflight, and that the prophages present are novel.

Phage↗

Small-Scale Dissipation in Binary-Species Transitional Mixing Layers

Motivated by large eddy simulation (LES) modeling of supercritical turbulent flows, transitional states of databases obtained from direct numerical simulations (DNS) of binary-species supercritical temporal mixing layers were examined to understand the subgrid-scale dissipation, and its variation with filter size. Examination of the DSN-scale domain- averaged dissipation confirms previous findings that, out of the three modes of viscous, temperature and species-mass dissipation, the species-mass dissipation is the main contributor to the total dissipation. The results revealed that the percentage of species-mass by total dissipation is nearly invariant across species systems and initial conditions. This dominance of the species-mass dissipation is due to high-density-gradient magnitude (HDGM) regions populating the flow under the supercritical conditions of the simulations; such regions have also been observed in fully turbulent supercritical flows. The domain average being the result of both the local values and the extent of the HDGM regions, the expectations were that the response to filtering would vary with these flow characteristics. All filtering here is performed in the dissipation range of the Kolmogorov spectrum, at filter sizes from 4 to 16 times the DNS grid spacing. The small-scale (subgrid scale, SGS) dissipation was found by subtracting the filtered-field dissipation from the DNS-field dissipation. In contrast to the DNS dissipation, the SGS dissipation is not necessarily positive; negative values indicate backscatter. Backscatter was shown to be spatially widespread in all modes of dissipation and in the total dissipation (25 to 60 percent of the domain). The maximum magnitude of the negative subgrid- scale dissipation was as much as 17 percent of the maximum positive subgrid- scale dissipation, indicating that, not only is backscatter spatially widespread in these flows, but it is considerable in magnitude and cannot be ignored for the purposes of LES modeling. The Smagorinsky model, for example, is unsuited for modeling SGS fluxes in the LES because it cannot render backscatter. With increased filter size, there is only a modest decrease in the spatial extent of backscatter. The implication is that even at large LES grid spacing, the issue of backscatter and related SGS-flux modeling decisions are unavoidable. As a fraction of the total dissipation, the small-scale dissipation is between 10 and 30 percent of the total dissipation for a filter size that is four times the DNS grid spacing, with all OH cases bunched at 10 percent, and the HN cases spanning 24 30 percent. A scale similarity was found in that the domain-average proportion of each small-scale dissipation mode, with respect to the total small-scale dissipation, is very similar to equivalent results at the DNS scale. With increasing filter size, the proportion of the small-scale dissipation in the dissipation increases substantially, although not quite proportionally. When the filter size increases by four-fold, 52 percent for all OH runs, and 70 percent for HN runs, of the dissipation is contained in the subgrid-scale portion with virtually no dependence on the initial conditions of the DNS. The indications from the dissipation analysis are that modeling efforts in LES of thermodynamically supercritical flows should be focused primarily on mass-flux effects, with temperature and viscous effects being secondary. The analysis also reveals a physical justification for scale-similarity type models, although the suitability of these will need to be confirmed in a posteriori studies.

Bellan, Josette↗

Spirochaete genome identified in red abalone sample represents a novel genus Candidatus Haliotispira gen. nov. within the order Spirochaetales

A fully assembled spirochaete genome was identified as a contaminating scaffold in our red abalone ( Haliotis rufescens ) genome assembly. In this paper, we describe the analysis of this bacterial genome. The assembled spirochaete genome is 3.25 Mb in size with 48.5 mol% G+C content. The proteomes of 38 species were compared with the spirochaete genome and it was discovered to form an independent branch within the family Spirochaetaceae on the phylogenetic tree. The comparison of 16S rRNA sequences and average nucleotide identity scores between the spirochaete genome with known species of different families in Spirochaetia indicate that it is an unknown species. Further, the percentage of conserved proteins compared to neighbouring taxa confirm that it does not belong to a known genus within Spirochaetaceae . We propose the name Candidatus Haliotispira prima gen. nov., sp. nov. based on its taxonomic placement and origin. We also tested for the presence of this species in different species of abalone and found that it is also present in white abalone ( Haliotis sorenseni ). In addition, we highlight the need for better classification of taxa within the class Spirochaetia .

Microbiology↗

Exabiome: Advancing Microbial Science through Exascale Computing

The Exabiome project seeks to improve the understanding of microbiomes through the development of methods for accelerating metagenomic science using exascale computing. This article gives an overview of scientific impact of the three components of the project: metagenome assembly, protein family detection, and comparative analysis of metagenomes. Exabiome developed MetaHipMer, the only metagenome assembler capable of scaling to full exascale systems. MetaHipMer has enabled ground-breaking assemblies on the Frontier supercomputer, with many scientific benefits, such as the discovery of rare species and viral genomes. To investigate protein families, Exabiome developed two exascale tools, PASTIS and HipMCL. Together, these can utilize exascale resources to understand the functional diversity of billions of dark matter proteins and novel protein families. For comparative analysis, Exabiome developed kmerprof, a tool that can be used to compare huge metagenomes for many different scientific purposes, for example, grouping human microbiomes according to body location.

59 BASIC BIOLOGICAL SCIENCES↗

Predicting the Dissolution Rate of Borosilicate Glasses using QSPR analysis based on molecular dynamics simulations

Quantitative Structure Property Relationship (QSPR) analysis based on molecular dynamics (MD) simulations is a promising approach for establishing the composition-property relationships of glass and other materials with complex structures. A series of 20 borosilicate and boroaluminosilicate glasses have been modeled by using MD simulations with recently developed effective potentials. Short- and medium-range structures of these glasses were analyzed and, based on these structural information, QSPR analysis of the initial dissolution rate (r0) was made and compared with measured r0 at 90°C and pH 9 using various structural descriptors such as percentage of bridging oxygen species, network connectivity and average ring size. The structural descriptors, Fnet, containing energetic information such as single bond strength and other structural information were also used. It was found that overall network connectivity, average ring size and Fnet give reasonable predictions of the r0 of studied glasses, given the conditions that the glasses are homogeneous and dissolve congruently. Modifying glass compositions to account preferential release of modifiers gives a better prediction for incongruently dissolving glasses. The results were compared with our recent work of predicting glass dissolution behavior from compositions using the topological-constraints-based models.

Du, Jincheng↗

Monitoring Avian Productivity and Survivorship at the Sandia Wetlands at Los Alamos National Laboratory (2014-2019)

Biologists at Los Alamos National Laboratory completed six years (2014–2019) of demographic monitoring of passerines (songbirds) during the breeding season in Los Alamos, New Mexico. We captured songbirds at a mist netting station located in the Sandia Wetlands in Sandia Canyon (Technical Areas 60 and 61). We identified, measured, and then banded captured birds with federal migratory bird bands. Banding operations took place between May and August of each year, with 10 mist netting sessions annually. We conducted this project as part of the implementation of the Biological Resources Management Plan. The project complies with the 2013 Memorandum of Understanding between the United States Fish and Wildlife Service (USFWS) and the United States Department of Energy regarding the implementation of Executive Order 13186. The overall number of birds and species captured was variable, and we saw no decreases over the course of six years in bird species diversity, abundance, or the percentage of breeding birds. Our results indicate that the Sandia Wetlands support numerous species of breeding birds, including species of conservation concern. We did not see a declining trend for the top 10 most-captured species or for any of the species of conservation concern over time; however, we need more years of data to make robust conclusions about population trends through time. Our results indicated that adult recapture rates at the Sandia Wetlands are at least twice as low when compared with estimated adult survival in migratory passerines from peer-reviewed literature. We also did not recapture any birds that were banded as juveniles in subsequent years throughout the entire six-year period. Low recapture rates for adults and the non-existent recapture rates for juveniles should be explored further. To accurately assess individual species survival rates for adults and juveniles using mark-recapture models, we need a longer dataset, which would allow for a more robust analysis.

59 BASIC BIOLOGICAL SCIENCES↗

Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets

Abstract Background Mass spectrometry-based proteomics can identify and quantify thousands of proteins from individual microbial species, but a significant percentage of these proteins are unannotated and hence classified as proteins of unknown function (PUFs). Due to the difficulty in extracting meaningful metabolic information, PUFs are often overlooked or discarded during data analysis, even though they might be critically important in functional activities, in particular for metabolic engineering research. Results We optimized and employed a pipeline integrating various “guilt-by-association” (GBA) metrics, including differential expression and co-expression analyses of high-throughput mass spectrometry proteome data and phylogenetic coevolution analysis, and sequence homology-based approaches to determine putative functions for PUFs in Clostridium thermocellum . Our various analyses provided putative functional information for over 95% of the PUFs detected by mass spectrometry in a wild-type and/or an engineered strain of C. thermocellum . In particular, we validated a predicted acyltransferase PUF (WP_003519433.1) with functional activity towards 2-phenylethyl alcohol, consistent with our GBA and sequence homology-based predictions. Conclusions This work demonstrates the value of leveraging sequence homology-based annotations with empirical evidence based on the concept of GBA to broadly predict putative functions for PUFs, opening avenues to further interrogation via targeted experiments.

09 BIOMASS FUELS↗

Transcriptome Mining Provides Insights into Cell Wall Metabolism and Fiber Lignification in Agave tequilana Weber

Resilience of growing in arid and semiarid regions and a high capacity of accumulating sugar-rich biomass with low lignin percentages have placed Agave species as an emerging bioenergy crop. Although transcriptome sequencing of fiber-producing agave species has been explored, molecular bases that control wall cell biogenesis and metabolism in agave species are still poorly understood. Here, through RNAseq data mining, we reconstructed the cellulose biosynthesis pathway and the phenylpropanoid route producing lignin monomers in A. tequilana, and evaluated their expression patterns in silico and experimentally. Most of the orthologs retrieved showed differential expression levels when they were analyzed in different tissues with contrasting cellulose and lignin accumulation. Phylogenetic and structural motif analyses of putative CESA and CAD proteins allowed to identify those potentially involved with secondary cell wall formation. RT-qPCR assays revealed enhanced expression levels of AtqCAD5 and AtqCESA7 in parenchyma cells associated with extraxylary fibers, suggesting a mechanism of formation of sclerenchyma fibers in Agave similar to that reported for xylem cells in model eudicots. Overall, our results provide a framework for understanding molecular bases underlying cell wall biogenesis in Agave species studying mechanisms involving in leaf fiber development in monocots.

59 BASIC BIOLOGICAL SCIENCES↗

Iterative techniques to estimate signature vectors for mixture processing of multispectral data

Two methods for obtaining the required spectral signatures for a particular mixture model are considered. For the model considered, the spectral signatures become signature vectors. The first method is based upon determination of the signature vectors in such a way that a measure of the inconsistency between the mixture model and the observed data is minimized. The second method is based upon determination of the signature vectors in such a way that the estimated mean percentage coverage of individual species matches apriori or ground truth estimates. The two methods proposed are applied to actual multispectral data in order to verify the concepts presented.

Salvato, P., Jr.↗

Spaceborne Remote Sensing of Aerosol Type: Global Distribution, Model Evaluation and Translation into Chemical Speciation

It is essential to evaluate and refine aerosol classification methods applied to passive satellite remote sensing. We have developed an aerosol classification algorithm (called Specified Clustering and Mahalanobis Classification, SCMC) that assigns an aerosol type to multi-parameter retrievals by spaceborne, airborne or ground-based passive remote sensing instruments [1]. The aerosol types identified by our scheme are pure dust, polluted dust, urban-industrialdeveloped economy, urban-industrialdeveloping economy, dark biomass smoke, light biomass smoke and pure marine. We apply the SCMC method to inversions from the ground-based AErosol RObotic NETwork (AERONET [2]) and retrievals from the space-borne Polarization and Directionality of Earths Reflectances instrument (POLDER, [3]). The POLDER retrievals that we use differ from the standard POLDER retrievals [4] as they make full use of multi-angle, multispectral polarimetric data [5]. We analyze agreement in the aerosol types inferred from both AERONET and POLDER and evaluate GEOS-Chem [6] simulations over the globe. Finally, we use in-situ observations from the SEAC4RS airborne field experiment to bridge the gap between remote sensing-inferred qualitative SCMC aerosol types and their corresponding quantitative chemical speciation. We apply the SCMC method to airborne in-situ observations from the NASA Langley Aerosol Research Group Experiment (LARGE, [7]) and the Differential Aerosol Sizing and Hygroscopicity Spectrometer Probe (DASH-SP, [8]) instruments; we then relate each coarsely defined SCMC type to a sum of percentage of individual aerosol species, using in-situ observations from the Particle Analysis by Laser Mass Spectrometry (PALMS, [9]), the Soluble Acidic Gases and Aerosol (SAGA, [10]), and the High - Resolution Time - of - Flight Aerosol Mass Spectrometer (HR ToF AMS, [11]).

airborne↗

Characterization of Forested Landscapes From Remotely Sensed Data Using Fractals and Spatial Autocorrelation

The characterization of forested areas is frequently required in resource management practice. Passive remotely sensed data, which are much more accessible and cost effective than are active data, have rarely, if ever, been used to characterize forest structure directly, but rather they usually focus on the estimation of indirect measurement of biomass or canopy coverage. In this study, some spatial analysis techniques are presented that might be employed with Landsat TM data to analyze forest structure characteristics. A case study is presented wherein fractal dimensions, along with a simple spatial autocorrelation technique (Moran s I), were related to stand density parameters of the Oakmulgee National Forest located in the southeastern United States (Alabama). The results of the case study presented herein have shown that as the percentage of smaller diameter trees becomes greater, and particularly if it exceeds 50%, then the canopy image obtained from Landsat TM data becomes sufficiently homogeneous so that the spatial indices reach their lower limits and thus are no longer determinative. It also appears, at least for the Oakmulgee forest, that the relationships between the spatial indices and forest class percentages within the boundaries can reasonably be considered linear. The linear relationship is much more pronounced in the sawtimber and saplings cases than in samples dominated by medium sized trees (poletimber). In addition, it also appears that, at least for the Oakmulgee forest, the relationships between the spatial indices and forest species groups (Hardwood and Softwood) percentages can reasonably be considered linear. The linear relationship is more pronounced in the forest species groups cases than in the forest classes cases. These results appear to indicate that both fractal dimensions and spatial autocorrelation indices hold promise as means of estimating forest stand characteristics from remotely sensed images. However, additional work is needed to confirm that the boundaries identified for Oakmulgee forest and the linear nature of the relationship between image complexity indices and forest characteristics are generally evident in other forests. In addition, the effects of other parameters such ,as topographic relief and image distortion due to sun angle and cloud cover, for example, need to be examined.

Al-Hamdan, Mohammad Z.↗

CO2 refixation is higher in leaves of woody species with high mesophyll and stomatal resistances to CO2 diffusion

Abstract The percentage of respiratory and photorespiratory CO2 refixed in leaves (Pr) represents part of the CO2 used in photosynthesis. The importance of Pr as well as differences between species and functional types are still not well investigated. In this study, we examine how Pr differs between six temperate and boreal woody species: Betula pendula, Quercus robur, Larix decidua, Pinus sylvestris, Picea abies and Vaccinium vitis-idaea. The study covers early and late successional species, deciduous broadleaves, deciduous conifers, evergreen conifers and evergreen broadleaves. We investigated whether some species or functional types had higher refixation percentages than others, whether leaf traits could predict higher Pr and whether these traits and their impact on Pr changed during growing seasons. Photosynthesis CO2 response (A/Ci)-curves, measured early, mid and late season, were used to estimate and compare Pr, mesophyll resistance (rm) and stomatal resistance (rs) to CO2 diffusion. Additionally, light images and transmission electron microscope images were used to approximate the fraction of intercellular airspace and cell wall thickness. We found that evergreens, especially late successional species, refixed a significantly higher amount of CO2 than the other species throughout the entire growing season. In addition, rm, rs and leaf mass per area, traits that typically are higher in evergreen species, were also significantly, positively correlated with Pr. We suggest that this is due to higher rm decreasing diffusion of (photo) respiratory CO2 out of the leaf. Cell wall thickness had a positive effect on Pr and rm, while the fraction of intercellular airspace had no effect. Both were significantly different between evergreen conifers and other types. Our findings suggest that species with a higher rm use a greater fraction of mitochondria-derived CO2, especially when stomatal conductance is low. This should be taken into account when modeling the overall CO2 fertilization effect for terrestrial ecosystems dominated by high rm species.

59 BASIC BIOLOGICAL SCIENCES↗